Warren and Matt, Thanks so much for your help. I must be using the stock glibc because "set max_threads, 1" allows me to ray trace without crashing. I will tell my system administrator to patch glibc. Do you know where I should look for the patch?
My debian/testing system at home also has trouble ray tracing, especially with sticks. When it fails I get a segmentation fault. Is my problem at home also due to an unpatched glibc? The error message is: /usr/bin/pymol: line 7: 32460 Segmentation fault python /usr/lib/python2.3/site-packages/pymol/__init__.py $* Thanks for creating such a great program, Morri On Tue, 20 Jan 2004 18:35:07 -0800 "Warren L. DeLano" wrote: > Morri, > > (First, thanks Matt for the great diagnostic advice!) > > This sounds to me like a potential threading deadlock, possible > due to the broken threading in RedHat 9. Are you using the stock > version or have you patched glibc? > > If you haven't patched your RedHat 9, then one way to be sure > this is the problem is to "set max_threads, 1" before issuing the ray > command. If PyMOL doesn't hang, then you've found the culprit. > > If have already patched your RH9, then let's do some more work > to determine what's going on... > > Cheers, > Warren > > -- > mailto:war...@delanoscientific.com > Warren L. DeLano, Ph.D. > Principal Scientist > DeLano Scientific LLC > Voice (650)-346-1154 > Fax (650)-593-4020 > > > -----Original Message----- > > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > > ad...@lists.sourceforge.net] On Behalf Of Matt Franklin > > Sent: Tuesday, January 20, 2004 6:25 PM > > To: Morri Feldman > > Cc: pymol-users > > Subject: Re: [PyMOL] Ray Tracing Crash > > > > Morri Feldman wrote: > > > I am running pymol .93. When I try to ray trace a scene, the gui > shows > > a > > > white status bar that moves halfway across the screen and then > freezes. > > > After this the GUI is frozen and must be killed. No error messages > are > > > shown. The computer is running RedHat 9 and has 4 processors. Has > > > anyone else experienced this problem? Do you have any solutions? > > > > > > This message may double post because I accidentally tried to post it > > from > > > my other email account. Sorry > > > > > > Thanks, Morri > > > > > > Morri Feldman > > > > > > > Hi Morri - > > > > The progress bar for raytracing doesn't move linearly - the first half > > of the bar is covered fairly quickly, then more slowly, then very > > slowly, then the last fifth is usually covered in one jump. Are you > > sure you just aren't being impatient? Try raytracing a very simple > > scene, like a single amino acid in spheres mode, to see if it hangs > > then. Also try raytracing parts of your scene in case some funny bit > of > > your molecule is causing this problem. Finally, try reducing the > > complexity of your surfaces and/or spheres: "set surface_quality, -1" > (0 > > is the default). > > > > Feel free to contact me directly - I'm local! (Although Warren will > be > > more helpful...) > > > > - Matt > > > > > > -- > > Matthew Franklin Phone:(650)225-4596 > > Postdoctoral Researcher Fax:(650)225-3734 > > Genentech, Inc. > > 1 DNA Way, South San Francisco, CA 94080 > > > > > > > > ------------------------------------------------------- > > The SF.Net email is sponsored by EclipseCon 2004 > > Premiere Conference on Open Tools Development and Integration > > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. > > http://www.eclipsecon.org/osdn > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > ------------------------------------------------------- > The SF.Net email is sponsored by EclipseCon 2004 > Premiere Conference on Open Tools Development and Integration > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. > http://www.eclipsecon.org/osdn > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > Morri Feldman
